The authors gratefully acknowledge Ms. Christine Stefani for performing the XRPD measurements. Marian Schu&#776;ch and Rebekka Kuiter (State Academy of Art and Design Stuttgart) are acknowledged for the pictures of the tile (Fig. 7).

1. Sample Preparation
<ol>
	<li>Collection of material
	<ol>
		<li>Carefully pick a small amount (less than 1 mg) of sample 1 under a digital microscope using a scalpel and tweezers from settings of opaque blue-green cabochons on a historic clasp, belonging to the collection of the Rosgartenmuseum Konstanz (RMK-1964.79) (Figure 6).</li>
		<li>Carefully scratch a few mg of sample 2 with a scalpel from the surface of a glazed ceramic tile, dating at early modern times, manufactured in Southern Germany, with size of 41 x 29 x 3.5 cm, and part of the collection of Landesmuseum W&#252;rttemberg (no. E 3004) (Figure 7). 
		Note: The tile was stored from the 1980s until 2004 in wooden cupboards. The backside heavily suffers thecotrichite efflorescence occurring as a phase-pure product (Figure 7b).</li>
	</ol>
	</li>
	<li>Preparation of the sample holders
	<ol>
		<li>Grind both samples carefully with a pestle in a small agate mortar.</li>
		<li>Distribute sample 1, which consists of few agglomerated grains (&#60;1 mg), between two thin X-ray transparent polyimide foils and mount them on a transmission sample holder with a central opening of 8 mm diameter. Fix the transmission sample holder on the &#952;-circle of the diffractometer.</li>
		<li>Fill sample 2 (approx. 5 mg) in a borosilicate glass capillary of 0.5 mm diameter.
		<ol>
			<li>To do so, place a small amount of powder into the funnel of the capillary using a spatula. Then move the powder down to the tip of the capillary with the help of an electric vibrator. Compact the powder by placing the capillary in a thick walled glass tube and tap it manually on the desk.</li>
			<li>Continue until a filling height of about 3 cm is reached. Cut the glass capillary carefully at a height of approximately 4 cm using a thin corundum blade and seal the open end using a lighter.</li>
			<li>Place a small amount of beeswax in the opening of a brass pin and melt it using a soldering iron. Then place the capillary in the molten wax and keep it upright until solidification. Mount the brass pin on a goniometer head and fix the goniometer head on the &#952;-circle of the diffractometer.</li>
			<li>Finally, center the mounted capillary by iteratively aligning the four degrees of freedom of the goniometer head (two rotations using bending slides and two translations using XY translation stages) manually with a wrench supported by a digital camera projection superimposed with a cross hair.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Data Collection
<ol>
	<li>For the laboratory XRPD patterns of samples 1 (Figure 8) and 2 (Figure 9) at room temperature use a high-resolution powder diffractometer (with primary beam Johann-type Ge(111) monochromator for Cu-K&#945;1-radiation) which is equipped with a linear position sensitive silicon strip detector with an opening of approximately 12&#176; 2&#952;.
	<ol>
		<li>Measure sample 1 for 20 hr in the range from 5-85&#176; 2&#952; with a step width of 0.015&#176; 2&#952; in transmission mode (Scan mode: Transmission; Scan type: 2ThetaOmega; Omega mode: Moving; PSD Mode: Moving). Turn rotation on in order to achieve better particle statistics.</li>
		<li>Record sample 2 for a period of 6 hr covering the range 5-60&#176; in 2&#952; with a step size of 0.015&#176; in Debye-Scherrer mode (Scan mode: Debye Scherrer; Scan type: 2Theta; Omega mode: Stationary; PSD Mode: Moving). Turn rotation on in order to achieve better particle statistics.</li>
	</ol>
	</li>
</ol>
3. Crystal Structure Determination and Refinement
Note: For the determination and refinement of the crystal structures of samples 1 and 2, a complex computer program is used11. It is either run by a graphical user interface or by text based input files. The latter make use of a sophisticated scripting language. Sample input files of the different stages of the structural analysis using sample 1 are listed in Tables S1, S2, S4-S8. The general procedure is identical for sample 2.
<ol>
	<li>Peak search
	<ol>
		<li>Perform an automatic peak search using the first and second derivatives of Savitzky-Golay polynoms of low order (Figure 10) according to manufacturer&#8217;s protocol by setting the convolute range on the order of 1-1.5 times the full width at half maximum of the Bragg reflections (0.12&#176; 2 &#952; for sample 1), adjusting the noise threshold to 1.5-2 times the estimated standard deviation (1.74 for sample 1) and limiting the search for that part of the powder patterns which show clearly distinguishable peaks (5-66&#176; 2&#952; for sample 1) above the background.
		<ol>
			<li>Start the program by double clicking the icon. Click Load Scan Files. Pull down menu Select X-Y data files (*.xy). Double click on 1-GNM-4145-P4-Kapton.xy.</li>
			<li>Expand range 1-GNM-4145-P4-Kapton.xy. Click Emission profile | Load Emission profile | CuK1sharp.lam.</li>
			<li>Click button Automatically insert peaks. Unclick Remove K-Alpha 2 Peaks. Set Peak Width with slide bar to 0.12. Set Noise Threshold with slide bar to 1.74. Press button Add Peaks. Press Close.</li>
		</ol>
		</li>
		<li>Use the integrating property of the human eye and correct manually the automatically detected peaks by deleting non-Bragg peaks which obviously are due to counting statistics and adding peaks which are recognizable but hidden in the tails of other peaks. Set up indexing files with sets of 30 to 40 reflections for each sample using standard settings but allowing all crystal systems (Table S1).
		<ol>
			<li>Zoom with mouse in the pattern, use mouse wheel to scroll. Open Peak Details window by pressing F3. Set peaks by pressing left mouse button. Delete peaks by pressing F9. Close Peak Details window.</li>
			<li>Click on Peaks Phase. Mark all peaks yellow by clicking on Position. Left click in the yellow marked column. Click Copy all/selection | Create Indexing range. Deselect range 1-GNM-4145-P4-Kapton.xy. Select range Indexing. Select all Bravais lattices (click Use to highlight the list and set a tick mark). 
			&#160;</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Indexing
	<ol>
		<li>For indexing apply the &#8220;iterative use of singular value decomposition&#8221; algorithm12 (Table S2) until finding a primitive tetragonal unit cell for sample 1 and a primitive monoclinic lattice for sample 2 (see Table 1 for unit cell parameters).
		<ol>
			<li>Press Run button (F6). Press Yes to keep indexing solutions. Press Solutions button. Highlight first solution by left clicking button 1. Right click on the highlighted (yellow) solution. Click Copy all/selection. Deselect range Indexing. Select range 1-GNM-4145-P4-Kapton.xy. 
			Note: Other unit cells showing a high figure of merit all have multiple volumes but higher numbers of unobserved reflections as compared to the ones listed in Table 1. The program automatically suggests the most probable space groups based on the observed reflection extinctions which is P42/n (86) for sample 1 and P21/a for sample 2 (Figure 11).</li>
		</ol>
		</li>
		<li>Confirm these findings manually by searching for extinctions using the International Tables of Crystallography Volume A13 (Table S3). Estimate the number of formula units per unit cell from average volume increments to Z = 8 for sample 1 and Z = 4 for sample 2.</li>
	</ol>
	</li>
	<li>Whole powder pattern fitting
	<ol>
		<li>Perform whole powder pattern fitting according to Pawley14 for both powder patterns. For the description of the peak profiles, use the fundamental parameter (FP) approach15 (Figure 12). Model the background by orthogonal Chebychev polynomials of higher order (typically 8) and an additional 1/X term describing the air scattering at low diffraction angles. Set the Lorenz-Polarization factor to 27.3 which is the Bragg angle for the Ge(111) monochromator using Cu-K&#945;1 radiation. Table S4 contains all relevant input parameters.
		<ol>
			<li>Press Add hkl Phase. Expand range 1-GNM-4145-P4-Kapton.xy. Expand hkl_Phase. Click Indexing Details | Paste Indexing details. Click Background. Change Order to 8 (refine). Tick 1/X Bkg (refine).</li>
			<li>Click Instrument. Set Primary radius (mm) to 217.5. Set Secondary radius (mm) to 217.5. Tick Point detector. Tick Receiving Slit Width, value of 0.1 (fix). Tick Full Axial Model. Set Source length (mm) to 6 (fix). Set Sample length (mm) to 6 (fix). Set RS length (mm) to 6 (fix).</li>
			<li>Click Corrections. Tick Zero error, value to 0 (refine). Tick LP factor, value to 27.3 (fix). Click Miscellaneous. Set Conv. Steps to 2. Tick Start X, value 8. Tick Finish X, value 75. Click Peaks Phase | Delete Peaks Phase | Yes.</li>
			<li>Click hkl_Phase | Microstructure. Tick Cry Size L, value to 200 (refine). Tick Cry Size G, value to 200 (refine). Tick Strain L, value to 0.1 (refine). Tick Strain G, value to 0.1 (refine). Press Run button (F6).</li>
		</ol>
		</li>
		<li>&#160;Create a list of Bragg peaks suitable for Charge Flipping6. Click hkl_Phase. Click Charge-Flipping output. Tick A file for CF, value CF.A. Tick hkl file for CF, value CF.hkl. Press Run button (F6). Pull down menu File | Export to INP file. File name, value Pawley.INP. Press Save. 
		Note: For the consecutive structure determination, keep all instrument, peak shape and lattice parameters fixed.</li>
	</ol>
	</li>
	<li>Crystal Structure determination 
	Note: A combination of three methods (used in an iterative manner) is used to determine the crystal structures of samples 1 and 2.
	<ol>
		<li>Firstly, use the method of Charge Flipping6 supported by the inclusion of the tangent formula16 (Figure 13) to find the positions of most of the heavier atoms. Delete observed reflections with a d-spacing smaller than 1.28 (for sample 1) and extend the calculated sphere to a d-spacing of 0.9. All necessary parameters are listed in Table S5. Pick atoms with recognizable electron density from the resulting list, correct falsely assigned atom types of similar scattering power like carbon, oxygen or nitrogen manually.
		<ol>
			<li>Pull down File File | Close All - Confirm by clicking Yes. Pull down Launch Launch | Launch Kernel.</li>
			<li>Pull down Launch Launch | Set INP File. Select CF.INP (prepared input text file, listed in Table S5). Confirm by clicking Open. Press Run button (F6). Press STOP button (F8) after approx. 20,000 cycles. Confirm Charge flipping finished by pressing Yes.</li>
			<li>Press Temporary output window displaying selected atoms in z-matrix format button. Press Cloud options dialog button. Set N to pick to 45. Tick With Symmetry. Press Pick button. Copy temporary output and save it to a text file called FirstGuess.str. Close the charge flipping graphics window.</li>
		</ol>
		</li>
		<li>Secondly, apply the global optimization method of simulated annealing7,17 (Figure 14) to find the positions of all missing non-hydrogen atoms (mainly the carbon atoms of the formate/acetate groups). Use the automatic annealing scheme provided by the software. Subject only the scale factor and the positional and/or occupational parameters of selected atoms to simulated annealing. For sample 1, merge sodium and oxygen atoms within a radius of 1.1 &#197; to detect special positions (Table S6).
		<ol>
			<li>Pull down Launch Launch | Set INP File. Select SA.INP (prepared input text file, listed in Table S6). Confirm by clicking Open. Press Run button (F6). Press STOP button (F8) after several thousand cycles. Confirm Update input file by pressing Yes.</li>
		</ol>
		</li>
		<li>Thirdly, turn off simulated annealing and switch to Rietveld5 refinement mode by commenting out the command Auto_T(0.1). Fix all confirmed positional parameters. Include the calculation of a difference-Fourier map (Fobs-Fcalc) (Figure 15, Table S7) to check for unaccounted electron density. Include the additionally found atoms in the atom list and refine the atomic positions and occupancies.
		<ol>
			<li>Pull down Launch Launch | Set INP File. Select Fourier_search_for_C.INP (prepared input text file, listed in Table S7). Confirm by clicking Open. Press Run button (F6). Inspect the two graphical output windows displaying the almost complete crystal structure and the difference Fourier map. 
			Note: Cycle the three structure solving methods iteratively in case of failure. If necessary, apply anti bumping constraints to light atoms (carbon and oxygen atoms) (see Table S7).</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Rietveld refinement
	<ol>
		<li>For the final crystal structure refinements of samples 1 and 2, use the Rietveld whole-pattern refinement method5 (Figure 16). In order to avoid meaningless atomic shifts of atoms in the acetic acid and nitrate groups of sample 2, employ so called soft constraints (also called restraints) based on idealized bond lengths and angles. Calculate idealized positions of the missing hydrogen atoms using standard software18 (Table S8).</li>
		<li>Refine isotropic atomic displacement parameters for the non-hydrogen atoms of each crystal structure. In case of sample two, model the apparent anisotropy of the width of the Bragg reflections caused by microstrain by including symmetry adapted spherical harmonics of second order.</li>
		<li>Finally create plots of projections of the crystal structures of sample 1 (Figure 17) and sample 2 (Figure 18) and the two crystallographic information files (CIFs) which from now on can be used for full quantitative phase analysis. An example of such a full quantitative analysis is given in Figure 19 using the crystal structure of sample 1.</li>
	</ol>
	</li>
</ol>

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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+New+Method+of+X-Ray+Crystal+Analysis.">A New Method of X-Ray Crystal Analysis.</a> Phys. Rev. 10 (6), 661-696 (1917).</li><li>Rietveld, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+profile+refinement+method+for+nuclear+and+magnetic+structures.">A profile refinement method for nuclear and magnetic structures.</a> J. Appl. Cryst. 2, 65-71 (1969).</li><li>Oszlanyi, G., Suto, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ab+initio+structure+solution+by+charge+flipping.">Ab initio structure solution by charge flipping.</a> Acta Crystallogr. Sect. A. 60 (2), 134-141 (2004).</li><li>Newsam, J. M., Deem, M. W., Freeman, C. M., Prince, E., Stalick, J. 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Chem. 54 (6), 2638-2642 (2015).</li><li>Wahlberg, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystal+Structure+of+Thecotrichite,+an+Efflorescent+Salt+on+Calcareous+Objects+Stored+in+Wooden+Cabinets.">Crystal Structure of Thecotrichite, an Efflorescent Salt on Calcareous Objects Stored in Wooden Cabinets.</a> Cryst. Growth Des. 15 (6), 2795-2800 (2015).</li><li>Eggert, G., Fischer, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gef&#228;hrliche+Nachbarschaft:+Durch+Glas+induzierte+Metallkorrosion+an+Museums-Exponaten+-+Das+GIMME-Projekt.">Gef&#228;hrliche Nachbarschaft: Durch Glas induzierte Metallkorrosion an Museums-Exponaten - Das GIMME-Projekt.</a> Restauro. 1, 38-43 (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> TOPAS (current version 5.0). , (2015).</li><li>Coelho, A. 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The authors have nothing to disclose.

XRPD is a suitable technique for conservation research as it is non-destructive, fast and easy-to-use. XRPD data can be used in routine qualitative analysis, owing to the fact that the powder pattern is a fingerprint signature to the corresponding crystal structure. The biggest advantage of XRPD over other analytic techniques is the ability of performing simultaneous qualitative and quantitative analysis of crystalline constituents in mixtures by using the Rietveld refinement method5. Moreover, the presence of...

Conservation science applies scientific (often chemical) methods in the conservation of artifacts. This includes investigations of the production of artifacts (&#39;technical art history&#39;: How was it made at that time?) and their decay pathways as a prerequisite to develop proper conservation treatments. Oftentimes these studies deal with metal organic salts like carbonates, formates and acetates. Some of them have been deliberately manufactured using suitable compounds (e.g., vinegar), others derive from deterioration reactions with the atmosphere (carbon dioxide or carbonyl compounds from indoor air pollution)1. As a matter of fact, the crystal structures of many of these corrosion materials are still unknown. This is an unfortunate fact, since the knowledge of the geometrical structure helps conservation science to better understand production and decay reactions and to allow for full quantitative analysis in the case of mixtures.
Under the condition that the material of interest forms single crystals of sufficient size and quality, single crystal diffraction is the method of choice for the determination of the crystal structure. If these boundary conditions are not fulfilled, powder diffraction is the closest alternative. The biggest drawback of powder diffraction as compared to single crystal diffraction lies in the loss of the orientational information of the reciprocal d-vector d* (scattering vector). In other words, the intensity of a single diffraction spot is smeared over the surface of a sphere. This can be considered a projection of the three-dimensional diffraction (= reciprocal) space onto the one dimensional 2&#952;-axis of the powder pattern. As a consequence, scattering vectors of different direction but equal or similar length, overlap systematically or accidentally making it difficult or even impossible to separate these reflections2 (Figure 1). This is also the main reason why powder diffraction, despite its early invention just four years after the first single crystal experiment3,4, was mainly used for phase identification and quantification for more than half a century. Nevertheless, the information content of a powder pattern is huge as can be easily deduced from Figure 2. The real challenge, however, is to reveal as much information as possible in a routine way.
A crucial step towards this goal, without any doubt, was the idea from Hugo Rietveld in 19695 who invented a local optimization technique for crystal structure refinement from powder diffraction data. The method does not refine single intensities but the entire powder pattern against a model of increasing complexity, thus taking the peak overlap intrinsically into account. From that time on, scientists using powder diffraction techniques were no longer limited to data analysis by methods developed for single crystal investigation. Several years after the invention of the Rietveld method, the power of the powder diffraction method for ab-initio structure determinations was recognized. Nowadays, almost all branches of natural sciences and engineering use powder diffraction to determine more and more complex crystal structures, although the method can still not be regarded as routine. Within the last decade, a new generation of powder diffractometers in the laboratory was designed providing high resolution, high energy and high intensity. Better resolution immediately leads to better peak separation while higher energies fight absorption. The benefit of a better peak profile description based on fundamental physical parameters (Figure 3) are more accurate intensities of Bragg reflection allowing for more detailed structural investigations. With modern equipment and software even microstructural parameters like domain sizes and microstrain are routinely deduced from powder diffraction data.
All algorithms for crystal structure determination from powder diffraction data use single peak intensities, the entire powder pattern or a combination of both. The conventional single crystal reciprocal space techniques often fail due to an unfavorable ratio between available observations and structural parameters. This situation changed dramatically with the introduction of the &#34;charge flipping&#34; technique6 (Figure 4) and the development of global optimization methods in direct space, of which the simulated annealing technique7 (Figure 5) is the most prominent representative. In particular, the introduction of chemical knowledge into the structure determination process using rigid bodies or the known connectivity of molecular compounds concerning bond lengths and angles strongly reduces the number of necessary parameters. In other words, instead of three positional parameters for every single atom, only the external (and few internal) degrees of freedom of groups of atoms need to be determined. It is this reduction of structural complexity which makes the powder method a real alternative to single crystal analysis.
Two pioneering case studies of the authors8,9 proved that it is possible to solve complicated crystal structures of complex corrosion products using powder diffraction data. The superiority of the crystallographic studies compared to other approaches was demonstrated among others by the fact that in both cases the reported formulas had to be corrected after considering the solved crystal structures.
The occurrence of both materials under investigation in museums is related to their storage in wooden cabinets or exposed to other sources of carbonyl pollutants. The first material under investigation was sodium copper formate hydroxide oxide hydrate, Cu4Na4O(HCOO)8(OH)2&#8729;4H2O (sample 1), which forms on soda glass/copper alloy composite historic objects (e.g., enamels) in museum collections, exposed to formaldehyde and formic acid from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as &#34;glass induced metal corrosion&#34;10. For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2&#8729;6H2O (sample 2), was chosen. Thecotrichite is a frequently observed efflorescent salt forming needlelike crystallites on tiles and limestone museum objects, which are stored in oak cabinets and display cases. In this case, the wood acts as source for acetic acid which reacts with soluble chloride and nitrate salts from the artifact.
In the following part of the text, the individual steps of the structure determination process using powder diffraction data applied to corrosion products from conservation science are presented in detail.

<table><tbody><tr><td>Stadi-P&amp;nbsp;</td><td>Stoe &amp;amp; Cie GmbH</td><td></td><td>Powder Diffractometer</td></tr><tr><td>Mythen 1-K (450 &amp;mu;m)</td><td>Dectris Ltd.</td><td></td><td>Position Sensitive Detector</td></tr><tr><td>Mark tube borosilicate glass No. 50, 0.5 mm diameter</td><td>Hilgenberg GmbH</td><td>4007605</td><td>Low absorbing capillaries</td></tr><tr><td>Topas 5.0</td><td>Bruker AXS Advanced X-ray Solutions GmbH</td><td></td><td>Powder Diffraction Evaluation Software</td></tr></tbody></table>

x-ray powder diffraction in conservation science: towards routine crystal structure determination of corrosion products on heritage art objects

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder diffraction (XRPD) is presented in detail via two case studies.
The first material under investigation was sodium copper formate hydroxide oxide hydrate, Cu4Na4O(HCOO)8(OH)2&#8729;4H2O (sample 1) which forms on soda glass/copper alloy composite historic objects (e.g., enamels) in museum collections, exposed to formaldehyde and formic acid emitted from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as &#34;glass induced metal corrosion&#34;.
For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2&#8729;6H2O (sample 2), was chosen, which is an efflorescent salt forming needlelike crystallites on tiles and limestone objects which are stored in wooden cabinets and display cases. In this case, the wood acts as source for acetic acid which reacts with soluble chloride and nitrate salts from the artifact or its environment.
The knowledge of the geometrical structure helps conservation science to better understand production and decay reactions and to allow for full quantitative analysis in the frequent case of mixtures.

High resolution XRPD was used to determine the previously unknown crystal structures of two long-known corrosion products on historic objects. The samples were taken from two museum objects and carefully grinded before they were sealed in transmission and capillary sample holders (Figures 6, 7). Standard measurements using a state of the art laboratory high resolution powder diffractometer in transmission and Debye-Scherrer geometry using monochromatic X-rays were perform...

Watch this Scientific Journal Video about X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects at JoVE.com

X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects

Modern high resolution X-ray powder diffraction (XRPD) in the laboratory is used as an efficient tool to determine crystal structures of long-known corrosion products on historic objects.

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder ...

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Universidad de Cartagena UDEC

Research

JoVE Journal

Chemistry

15.8K Views.  Max-Planck-Institute for Solid State Research. Modern high resolution X-ray powder diffraction (XRPD) in the laboratory is used as an efficient tool to determine crystal structures of long-known corrosion products on historic objects.

Video: X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects

Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary interiors, design materials with novel properties, understand the mechanical behavior of materials exposed to very high stresses as in explosions or impacts. Synthesis and structural analysis of materials at extreme conditions of pressure and temperature entails remarkable technical challenges. In the laser heated diamond anvil cell (LH-DAC), very high pressure is generated between the tips of two opposing diamond anvils forced against each other; focused infrared laser beams, shined through the diamonds, allow to reach very high temperatures on samples absorbing the laser radiation. When the LH-DAC is installed in a synchrotron beamline that provides extremely brilliant x-ray radiation, the structure of materials under extreme conditions can be probed in situ. LH-DAC samples, although very small, can show highly variable grain size, phase and chemical composition. In order to obtain the high resolution structural analysis and the most comprehensive characterization of a sample, we collect diffraction data in 2D grids and combine powder, single crystal and multigrain diffraction techniques. Representative results obtained in the synthesis of a new iron oxide, Fe4O5 1 will be shown.

The laser heated diamond anvil cell combined with synchrotron micro-diffraction techniques allows researchers to explore the nature and properties of new phases of matter at extreme pressure and temperature (PT) conditions. Heterogeneous samples can be characterized in situ under high pressure by 2D mapping and combined powder, single-crystal and multigrain diffraction approaches.

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary ...

Engineering

High Pressure Single Crystal Diffraction at PX^2

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 &#177;0.006 &#197;, b = 8.761 &#177;0.004 &#197;, c = 5.248 &#177;0.001 &#197;, &#946; = 105.06 &#177;0.03&#186;, &#945; = &#947; = 90&#186;.

In this report, we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell at the GSECARS 13-BM-C beamline at the Advanced Photon Source. ATREX and RSV programs are used to analyze the data.

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the ...

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments

The equilibrium outcomes of ball mill grinding can dramatically change as a function of even tiny variations in the experimental conditions such as the presence of very small amounts of added solvent. To reproducibly and accurately capture this sensitivity, the experimentalist needs to carefully consider every single factor that can affect the ball mill grinding reaction under investigation, from ensuring the grinding jars are clean and dry before use, to accurately adding the stoichiometry of the starting materials, to validating that the delivery of solvent volume is accurate, to ensuring that the interaction between the solvent and the powder is well understood and, if necessary, a specific soaking time is added to the procedure. Preliminary kinetic studies are essential to determine the necessary milling time to achieve equilibrium. Only then can exquisite phase composition curves be obtained as a function of the solvent concentration under ball mill liquid assisted grinding (LAG). By using strict and careful procedures analogous to the ones here presented, such milling equilibrium curves can be obtained for virtually all milling systems. The system we use to demonstrate these procedures is a disulfide exchange reaction starting from the equimolar mixture of two homodimers to obtain at equilibrium quantitative heterodimer. The latter is formed by ball mill grinding as two different polymorphs, Form A and Form B. The ratio R = [Form B] / ([Form A] + [Form B]) at milling equilibrium depends on the nature and concentration of the solvent in the milling jar.

We present detailed procedures to produce experimental equilibrium curves of the phase composition as a function of solvent concentration in a solid state system under milling conditions.

The equilibrium outcomes of ball mill grinding can dramatically change as a function of even tiny variations in the experimental conditions such as the ...

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

In this report, we describe a detailed procedure for acquiring and processing&#160;x-ray microfluorescence (&#956;XRF), and Laue and powder microdiffraction two-dimensional (2D) maps at beamline 12.3.2 of the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory. Measurements can be performed on any sample that is less than 10 cm x 10 cm x 5 cm, with a flat exposed surface. The experimental geometry is calibrated using standard materials (elemental standards for XRF, and crystalline samples such as Si, quartz, or Al2O3 for diffraction). Samples are aligned to the focal point of the x-ray microbeam, and raster scans are performed, where each pixel of a map corresponds to one measurement, e.g., one XRF spectrum or one diffraction pattern. The data are then processed using the in-house developed software XMAS, which outputs text files, where each row corresponds to a pixel position. Representative data from moissanite and an olive snail shell are presented to demonstrate data quality, collection, and analysis strategies.

We describe a beamline setup meant to carry out rapid two-dimensional x-ray fluorescence and x-ray microdiffraction mapping of single crystal or powder samples using either Laue (polychromatic radiation) or powder (monochromatic radiation) diffraction. The resulting maps give information about strain, orientation, phase distribution, and plastic deformation.

In this report, we describe a detailed procedure for acquiring and processing&#160;x-ray microfluorescence (&#956;XRF), and Laue and powder ...

Synthesis and Discovery of Phosphonate-Based MOFs: A Solvothermal Approach

Discovery and Synthesis Optimization of Isoreticular Al(III) Phosphonate-Based Metal-Organic Framework Compounds Using High-Throughput Methods

High-throughput (HT) methods are an important tool for the fast and efficient screening of synthesis parameters and the discovery of new materials. This manuscript describes the synthesis of metal-organic frameworks (MOFs) from solution using an HT reactor system, resulting in the discovery of various phosphonate-based MOFs of the composition [Al2H12-x(PMP)3]Clx&#8729;6H2O (H4PMP = N,N &#39;-piperazine bis(methylenephosphonic acid)) for x = 4, 6, denoted as Al-CAU-60-xHCl, containing trivalent aluminum ions. This was accomplished under solvothermal reaction conditions by systematically screening the impact of the molar ratio of the linker to the metal and the pH of the reaction mixture on the product formation. The protocol for the HT investigation includes six steps: a) synthesis planning (DOE = design of&#160;experiment) within the HT methodology, b) dosing and working with in-house developed HT reactors, c) solvothermal synthesis, d) synthesis workup using in-house developed filtration blocks, e) characterization by HT powder X-ray diffraction, and f) evaluation of the data. The HT methodology was first used to study the influence of acidity on the product formation, leading to the discovery of Al-CAU-60&#8729;xHCl (x = 4 or 6).

Author Spotlight: Accelerating Discovery in Microporous Material Chemistry 

The targeted synthesis of new metal-organic frameworks (MOFs) is difficult, and their discovery depends on the knowledge and creativity of the chemist. High-throughput methods allow complex synthetic parameter fields to be explored quickly and efficiently, accelerating the process of finding crystalline compounds and identifying synthetic and structural trends.

High-throughput (HT) methods are an important tool for the fast and efficient screening of synthesis parameters and the discovery of new materials. This ...

X-ray Diffraction

Source: Faisal Alamgir, School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA
X-ray diffraction (XRD) is a technique used in materials science for determining the atomic and molecular structure of a material. This is done by irradiating a sample of the material with incident X-rays and then measuring the intensities and scattering angles of the X-rays that are scattered by the material. The intensity of the scattered X-rays are plotted as a function of the scattering angle, and the structure of the material is determined from the analysis of the location, in angle, and the intensities of scattered intensity peaks. Beyond being able to measure the average positions of the atoms in the crystal, information on how the actual structure deviates from the ideal one, resulting for example from internal stress or from defects, can be determined.
The diffraction of the X-rays, that is central to the XRD method, is a subset of the general X-ray scattering phenomena. XRD, which is generally used to mean can wide-angle X-ray diffraction (WAXD), falls under several methods that use the elastically scattered X-ray waves. Other elastic scattering based X-ray techniques include small angle X-ray scattering (SAXS), where the X-rays are incident on the sample over the small angular range of 0.1-100 typically). SAXS measures structural correlations of the scale of several nanometers or larger (such as crystal superstructures), and X-ray reflectivity that measures the thickness, roughness, and density of thin films. WAXD covers an angular range beyond 100.

X-Ray Diffraction for Determining Atomic and Molecular Structure

Source: Faisal Alamgir, School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA
X-ray diffraction (XRD) is a technique ...

Education

JoVE Science Education

Materials Engineering

X-ray Fluorescence (XRF)

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to generate spectroscopic information. X-ray fluorescence microscopy is a non-destructive imaging technique that uses the induced fluorescence emission of metals to identify and quantify their spatial distribution.

X-ray Fluorescence XRF: Elemental Analysis by Emitted Fluorescent X-Ray

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to ...

Analytical Chemistry

Growing Crystals for X-ray Diffraction Analysis

Source: Laboratory of Dr. Jimmy Franco - Merrimack College
X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms in a crystalline solid, which allows for the determination of the three-dimensional shape of a molecule or complex. Determining the three-dimensional structure of a compound is of particular importance, since a compound&#39;s structure and function are intimately related. Information about a compound&#39;s structure is often used to explain its behavior or reactivity. This is one of the most useful techniques for solving the three-dimensional structure of a compound or complex, and in some cases it may be the only viable method for determining the structure. Growing X-ray quality crystals is the key component of X-ray crystallography. The size and quality of the crystal is often highly dependent on the composition of the compound being examined by X-ray crystallography. Typically compounds containing heavier atoms produce a greater diffraction pattern, thus require smaller crystals. Generally, single crystals with well-defined faces are optimal, and typically for organic compounds, the crystals need to be larger than those containing heavy atoms. Without viable crystals, X-ray crystallography is not feasible. Some molecules are inherently more crystalline than others, thus the difficulty of obtaining X-ray quality crystals can vary between compounds. The growth of X-ray crystals is similar to the process of recrystallization that is commonly used for purifying compounds, but with an emphasis on producing higher quality crystals. Often, higher quality crystals can be obtained by allowing the crystallization process to proceed slowly, which may occur over the course of day or months.

Source: Laboratory of Dr. Jimmy Franco - Merrimack College
X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms ...

Organic Chemistry

Single Crystal and Powder X-ray Diffraction

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the structure of molecules. X-ray diffraction (XRD) experiments are routinely carried out with either single-crystal or powdered samples.
Single-crystal XRD:
Single-crystal XRD allows for absolute structure determination. With single-crystal XRD data, the exact atomic positions can be observed, and thus bond lengths and angles can be determined. This technique provides the structure within a single crystal, which does not necessarily represent the bulk of the material. Therefore, additional bulk characterization methods must be utilized to prove the identity and purity of a compound.
Powder XRD:
Unlike single-crystal XRD, powder XRD looks at a large sample of polycrystalline material and therefore is considered a bulk characterization technique. The powder pattern is considered a &#34;fingerprint&#34; for a given material; it provides information about the phase (polymorph) and crystallinity of the material. Typically, powder XRD is used to study minerals, zeolites, metal-organic frameworks (MOFs), and other extended solids. Powder XRD can also be used to establish bulk purity of molecular species.
Previously, we have seen how to grow X-ray quality crystals (see video in Essentials of Organic Chemistry series). Here we will learn the principles behind XRD. We will then collect both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the ...

X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects

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Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High Pressure Single Crystal Diffraction at PX^2

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

Discovery and Synthesis Optimization of Isoreticular Al(III) Phosphonate-Based Metal-Organic Framework Compounds Using High-Throughput Methods

X-ray Diffraction

X-ray Fluorescence (XRF)

Growing Crystals for X-ray Diffraction Analysis

Single Crystal and Powder X-ray Diffraction